The package “Rarity”, which allows calculating rarity indices for species and assemblages of species, is now available on the Comprehensive R Archive Network.

This package allows easy calculation of the new indices integrating rarity cut-offs; this flexibility allows fitting indices to the considered taxon, geographical area and/or spatial scale, i.e., to the considered database. See the rarity indices section for more details and examples.

This package simply requires occurrence data to calculate species rarity weights, and presence-absence or abundance data per site/assemblage/community to calculate rarity indices of sites/assemblages/species.

The Rarity package has two major functions:

  • rWeights – This function allows for calculating rarity weights for species with respect to the chosen rarity cut-off point. Multiscale rarity weights can also be calculated with this function. Classical weighting methods (e.g., the inverse of occurrence) can also be calculated with this function.
Weight assignation curve adjusted to an arbitrary rarity cut-off.
Weight assignation curve adjusted to an arbitrary rarity cut-off.

 

  • Irr – This function allows calculating rarity indices for assemblages of species, on the basis of the calculated rarity weights.

A PDF presentation of the package with examples is available on this link, although in French: rarity-package

References

Leroy B., Canard A. & Ysnel F. In Press. Integrating multiple scales in rarity assessments of invertebrate taxa. Diversity and Distributions

Leroy B., Pétillon J., Gallon R., Canard A. & Ysnel F. 2012. Improving occurrence-based rarity metrics in conservation studies by including multiple rarity cut-offs. Insect Conservation and Diversity 5:159-168.